An American jailed in Pakistan for the fatal shooting of two armed men was secretly working for the CIA and scouting a neighborhood when he was arrested, a disclosure likely to further frustrate U.S. government efforts to free the man and strain relations between two countries partnered in a fragile alliance in the war on terror.

Raymond Allen Davis [right], 36, had been working as a CIA security contractor for the U.S. consulate in Lahore, according to former and current U.S. officials, who spoke on condition of anonymity because they weren’t authorized to talk publicly about the incident.

Davis, a former Special Forces soldier who left the military in 2003, shot the men in what he described as an attempted armed robbery in the eastern city of Lahore as they approached him on a motorcycle. A third Pakistani, a bystander, died when a car rushing to help Davis struck him. Davis was reportedly carrying a Glock handgun, a pocket telescope and papers with different identifications.

The revelation that Davis was an employee of the CIA comes amid a tumultuous dispute over whether he is immune from criminal prosecution under international rules enacted to protect diplomats overseas. New protests in Pakistan erupted after The Guardian newspaper in London decided to publish details about Davis’ relationship with the CIA.

The U.S. had repeatedly asserted that Davis had diplomatic immunity and should have been released immediately. The State Department had claimed Davis was “entitled to full criminal immunity in accordance with the Vienna Convention” and was a member of the “technical and administrative staff” at the U.S. Embassy in Islamabad.

The Associated Press learned about Davis working for the CIA last month, immediately after the shootings, but withheld publication of the information because it could endanger his life while he was jailed overseas, with at least some protesters there calling for his execution as a spy.

The AP had intended to report Davis’ CIA employment after he was out of harm’s way, but the story was broken Sunday by The Guardian. The CIA asked The AP and several other U.S. media outlets to hold their stories as the U.S. tried to improve Davis’ security situation.

A U.S. official says Davis is being held at a jail on the outskirts of Lahore where there are serious doubts about whether the Pakistanis can truly protect him. The official says the Pakistanis have expressed similar concerns to the U.S.

The State Department said the Pakistani government was informed that Davis was a diplomat and entitled to immunity when he was assigned to the U.S. Embassy in Islamabad. “We notified the Pakistani government when he arrived in Islamabad,” department spokesman P.J. Crowley said.

Davis identified himself as a diplomat to police when he was arrested and “has repeatedly requested immunity” to no avail, Crowley said. The U.S. Embassy said he has a diplomatic passport and a visa valid through June 2012. It also said in a recent statement the U.S. had notified the Pakistani government of Davis’ assignment more than a year ago. However, a senior Pakistani intelligence official says that Davis’ visa application contained bogus U.S. contact information.

Since Pakistani authorities took the ex-Special Forces soldier into custody Jan. 27, U.S. officials said, the situation has slowly escalated into a crisis, threatening the CIA’s ability to wage a dangerous war against al-Qaida and militants. Some members of Congress have threatened to cut off the billions in funding to Pakistan if Davis isn’t released.

Davis was attached to the CIA’s Global Response Staff, which provides security overseas to agency bases and stations, former and current U.S. officials told the AP. In that role, he was assigned to protect CIA personnel. One of their duties includes protecting case officers when they meet with sources. On the day he was captured, he was familiarizing himself with the area.

“Davis is a protective officer, someone who provides security to U.S. officials in Pakistan,” the U.S official said. “Rumors to the contrary are simply wrong.”

In a YouTube video of local police interrogating him, Davis says he’s a consultant and he’s with the “RAO,” a reference to the American Regional Affairs Office. Davis also said at one point he was attached to the U.S. Embassy in Islamabad.

Working for the agency’s GRS comes with risks — sometimes fatal ones. The head of security at the CIA’s base in Khost, Afghanistan, was killed with six others in December 2009 after a suicide bomber detonated a powerful explosive under his belt.

The CIA has a major presence in Pakistan, where it runs the drone program in Islamabad and offensive operations against militants, al-Qaida and Pakistan’s spy agency, Inter-Services Intelligence.

Former and current U.S. officials say the Pakistanis might have been stalling to release Davis so he could be extensively questioned, hoping he could provide more information about CIA activities in the troubled country or possibly even identify other agency officers.

The senior Pakistani intelligence official told the AP the two men in the response vehicle that went to aid Davis, killing the bystander, have left the country. The official said the Pakistani government’s decision to let them leave was a concession to the U.S.

The U.S.-Pakistani partnership had begun to fray in recent months. In late 2010, a pair of civil lawsuits filed in the U.S. accused Pakistan’s spy chief of nurturing terrorists involved in the 2008 Mumbai attacks. Shortly after the lawsuits were filed, the name of the CIA’s top spy in Pakistan was publicly disclosed and his life threatened. He was eventually pulled out of the country in December, a month before the scheduled end of his tour.

A former CIA officer said militants have also threatened the children of ISI officers. And the CIA in recent years has become increasingly concerned about the safety of its officers in outlying areas like Lahore and Peshawar, a former senior U.S. intelligence source said. But the danger was more pronounced in Lahore, where the CIA learned there might be government elements willing to harm agency officers.

Former CIA officials said the agency officers could have been killed in 2009 when terrorists attacked an ISI compound in Lahore. CIA officers regularly met their counterparts at the compound but didn’t have a meeting scheduled the day of the attack.

Further inflaming tensions, the wife of one of the men Davis shot committed suicide. She had said she feared her husband’s killer would be freed without trial.

Military records show Davis, a Virginia native, served a decade in the Army, including five years with the 3rd Special Forces Group in Fort Bragg, N.C., home to the Green Berets.

Davis also worked for Xe Services, the security contractor formerly known as Blackwater.

Davis and his wife run a Las Vegas-registered company called Hyperion Protective Services. The address for its headquarters is a mailbox at a UPS store in a strip mall. The truth about Davis’ true employer briefly slipped out after a local television reporter in Colorado called his wife.

In a story posted on the website of Denver’s 9News, the wife provided the name and number of a “CIA spokesperson” in Washington, D.C. But the story was quickly taken down, edited and then reposted with new language eliminating any reference to the CIA.

The incident in Pakistan also raises serious questions about how an armed CIA employee could become involved in a fatal shooting with street bandits and allow himself to be captured. Former CIA officers say they were taught to make their way back to the safety of the embassy or consulate in potentially dangerous situations, but the circumstances could have made that impossible in Davis’ case.

Former CIA officials say this is not the first time an agency employee was detained in a foreign country. In the 1980s, a CIA officer with diplomatic immunity was abducted in Ethiopia after he was suspected of spying. The case was quietly resolved and the officer was eventually released.

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